AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_aquae_reg_100.orf -o012_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAA01502	110	Aquifex_aeolicus

Motif number 1

AAAACTGCTTACACAGGCGGCTTCTGTCCC	1	39	1	ACACAGGCGG	    0.993514	-72
CGCGTATCTATGATACGGGGACAGAAGCCG	1	56	0	TGATACGGGG	    0.994988	-55
CCCGTATCATAGATACGCGGTTTTAGCCCG	1	67	1	AGATACGCGG	    0.999257	-44
ATTTTATAGTAAATCCGCGGGCTAAAACCG	1	84	0	AAATCCGCGG	    0.996553	-27
          **********

Masking position 3
Map Score:   6.43443

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 45
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

TCATTTTAAAAAACTGCTTACACAGGCGGC	1	30	1	AAACTGCTTA	    0.980256	-81
ACGGGGACAGAAGCCGCCTGTGTAAGCAGT	1	42	0	AAGCCGCCTG	    0.989775	-69
CCGCGGGCTAAAACCGCGTATCTATGATAC	1	70	0	AAACCGCGTA	     0.99586	-41
ACGCGGTTTTAGCCCGCGGATTTACTATAA	1	81	1	AGCCCGCGGA	      0.9936	-30
          **********

Masking position 1
Map Score:   3.59632

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 84
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

          **********

No masking
Map Score:   -1.46782e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 4

          **********

No masking
Map Score:   -1.46782e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   -1.46782e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0